Facing a revolt from within his governing coalition, President Cyril Ramaphosa of South Africa announced on Sunday that he was suspending the country’s police minister and forming a commission to investigate allegations that the minister had protected allies within the country’s criminal underworld.

The allegations against the minister, Senzo Mchunu, were leveled a week ago by Lt. Gen. Nhlanhla Mkhwanazi, the top police commander in the southern province of KwaZulu-Natal. General Mkhwanazi said Mr. Mchunu had shut down a unit that investigated political killings in order to shield from scrutiny politicians, prosecutors, police officials and members of the judiciary with ties to a criminal syndicate.

The syndicate was behind several high-profile murders, General Mkhwanazi said.

Mr. Mchunu, a close ally of Mr. Ramaphosa, has denied the allegations against him. But the president was forced to act quickly as his administration became engulfed by weeks of growing political turmoil that threatened to cause the implosion of a fragile governing coalition formed with great hope and fanfare last year.

The commission will investigate whether law enforcement, intelligence and other criminal justice institutions have been infiltrated by criminal syndicates, Mr. Ramaphosa said. The inquiry will also explore whether senior justice system officials aided criminal activity or benefited from it, he said.

“We are affirming our commitment to the rule of law, to transparency and to accountability,” Mr. Ramaphosa said. “And we are also enhancing the work that is underway to build a South Africa in which all of our people are safe and secure.”

The allegations against Mr. Mchunu have presented the stiffest test of Mr. Ramaphosa’s ability to keep his government together amid growing anger from the Democratic Alliance, the second largest party in the coalition.